Contacts of the helix formed by residues 581 - 593 (chain C) in PDB entry 5MKE
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 581 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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579C PHE 5.0 0.2 - - - +
580C ASN* 1.3 134.1 + - + +
582C THR* 1.3 64.0 + - + +
583C MET* 3.0 23.3 - - + +
584C SER* 2.7 25.6 + - - -
585C GLN* 3.3 5.2 + - - +
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Residues in contact with THR 582 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581C ARG* 1.3 77.9 - - + +
583C MET* 1.3 68.0 + - - +
585C GLN* 3.0 10.5 + - - +
586C LEU* 3.0 42.2 + - - +
691C LEU* 6.2 3.6 - - + -
694C GLN* 3.9 24.5 - - - +
695C LYS* 6.1 2.5 - - - +
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Residues in contact with MET 583 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578C ASN* 4.7 4.7 + - + -
580C ASN* 3.3 35.9 - - + +
581C ARG* 3.0 19.0 - - + -
582C THR* 1.3 83.5 + - - +
584C SER* 1.3 61.3 + - - +
586C LEU* 3.5 11.2 + - - +
587C SER* 3.7 10.6 + - - -
595D LYS* 6.6 0.4 - - - -
599D GLY* 4.2 30.1 - - - +
600D PHE* 4.1 18.4 - - + -
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Residues in contact with SER 584 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578C ASN* 3.0 34.3 + - - +
579C PHE* 3.0 12.0 - - - -
580C ASN* 2.6 35.2 + - - -
581C ARG 2.7 15.3 + - - -
583C MET* 1.3 74.7 - - - +
585C GLN* 1.3 59.7 + - - -
586C LEU 3.6 0.2 + - - -
587C SER* 4.1 6.6 + - - -
588C THR* 3.7 11.6 + - - -
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Residues in contact with GLN 585 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581C ARG 3.3 5.9 + - - +
582C THR* 3.0 12.4 + - - +
584C SER* 1.3 79.6 - - - +
586C LEU* 1.3 67.9 + - + +
587C SER 3.5 0.2 - - - -
588C THR* 3.3 30.3 + - - +
589C THR* 4.2 6.9 + - - +
694C GLN* 5.0 13.2 - - - +
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Residues in contact with LEU 586 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582C THR* 3.0 32.4 + - - +
583C MET* 3.5 6.5 + - - +
584C SER 3.4 0.4 - - - -
585C GLN* 1.3 82.1 - - + +
587C SER* 1.3 64.1 + - - +
588C THR 3.1 1.8 - - - -
589C THR* 2.4 31.1 + - + +
590C MET* 3.4 2.8 + - - +
684C TYR* 5.8 5.6 - - + +
687C VAL* 4.4 17.8 - - + +
690C ASP* 5.9 1.3 - - - +
691C LEU* 3.5 51.1 - - + -
694C GLN* 6.2 0.7 - - - +
600D PHE* 4.7 13.5 - - + -
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Residues in contact with SER 587 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574C PHE* 4.6 16.0 - - - -
578C ASN* 4.8 9.9 - - - -
583C MET 3.7 7.9 + - - -
584C SER 4.1 4.0 + - - -
585C GLN 3.5 0.4 - - - -
586C LEU* 1.3 75.5 - - - +
588C THR* 1.3 66.8 + - - +
590C MET* 2.9 34.6 + - - +
591C SER* 3.8 3.5 + - - -
1008C PLM 5.3 1.2 + - - -
600D PHE* 3.6 28.2 - - - -
603D MET* 5.2 0.5 - - - -
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Residues in contact with THR 588 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507C TRP* 4.8 27.7 - - + +
584C SER 3.7 11.5 + - - -
585C GLN* 3.3 31.0 + - - +
586C LEU 3.1 0.4 - - - -
587C SER* 1.3 78.1 - - - +
589C THR* 1.3 67.0 + - + +
591C SER* 4.1 0.9 + - - -
592C ARG* 3.1 34.7 + - + +
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Residues in contact with THR 589 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585C GLN* 4.6 9.4 - - - +
586C LEU* 2.4 25.5 + - + +
588C THR* 1.3 78.1 - - + +
590C MET* 1.3 56.1 + - - +
592C ARG* 2.7 15.4 + - + -
593C CYS* 2.5 40.5 + - - -
686C GLU* 6.0 0.2 - - - -
687C VAL* 3.3 26.8 - - + +
690C ASP* 3.9 20.9 - - - +
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Residues in contact with MET 590 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586C LEU 3.4 1.5 + - - +
587C SER* 2.9 34.6 + - - +
589C THR* 1.3 83.2 + - - +
591C SER* 1.3 58.7 + - - +
593C CYS* 3.6 8.9 - - - -
594C ALA* 3.1 20.0 + - + +
687C VAL* 5.8 1.1 - - - -
1008C PLM 3.6 21.8 - - - +
600D PHE* 4.8 5.2 - - + -
603D MET* 4.0 22.0 - - + +
671D ILE* 3.5 37.2 - - + -
675D MET* 4.3 30.5 - - + +
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Residues in contact with SER 591 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587C SER 3.8 5.3 + - - -
588C THR 5.2 1.1 - - - -
590C MET* 1.3 79.1 - - - +
592C ARG* 1.3 60.5 + - - +
593C CYS 3.2 0.7 - - - -
594C ALA* 2.7 31.9 + - - +
595C LYS* 3.4 5.5 + - - +
598C PHE* 5.6 5.5 - - - -
1008C PLM 5.1 13.5 - - - -
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Residues in contact with ARG 592 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504C ARG* 4.9 25.8 - - - +
505C SER 4.5 8.9 + - - -
506C PHE* 5.7 5.6 - - - +
507C TRP* 4.0 22.0 - - - +
588C THR* 3.1 32.7 + - + +
589C THR* 2.7 18.4 + - + +
591C SER* 1.3 73.9 - - - +
593C CYS* 1.3 58.5 + - - +
595C LYS* 4.0 12.6 + - - +
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Residues in contact with CYS 593 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589C THR* 2.5 41.0 + - - +
590C MET* 3.6 10.3 - - - -
592C ARG* 1.3 71.6 - - - +
594C ALA* 1.3 57.1 + - - +
595C LYS* 3.1 7.9 + - - +
596C ASP* 3.9 11.8 + - - +
679C ILE* 4.8 2.3 - - - +
683C THR* 3.2 53.8 + - + +
684C TYR* 4.9 0.9 - - - -
686C GLU* 5.1 3.6 - - - +
687C VAL* 4.7 4.9 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il